A senior Israeli official dismissed the suggestion as "beyond pathetic."
The slain Lebanese official, Brigadier-General Wissam al-Hassan, was close to several Lebanese politicians who back the uprising in Syria and led several investigations into Syrian meddling in Lebanese affairs, including one that implicated Damascus and its Lebanese ally Hezbollah in the assassination of former prime minister Rafik al-Hariri in 2005.
Iran is Syria's most powerful regional ally.
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"This action was taken with the aim of sowing dissension among different currents and segments of the Lebanese people and was conducted by an element who has never had in mind the interests of the Lebanese people and government and who only strives for its own impure interests and goals," said a statement posted on the Iranian Foreign Ministry's website.
"Without a doubt the main enemy of the people of Lebanon and the region is the Zionist regime (Israel), which benefits from insecurity and instability in the region," ministry spokesman Ramin Mehmanparast said, according to the statement.
It offered no evidence for the suggestion of Israeli involvement.
Asked about Mehmanparast's remarks, Israeli Foreign Ministry spokesman Yigal Palmor said: "After the Iranian regime accused Israel of even the bad weather conditions prevailing in Iran, is there anything at all that they would not automatically blame on Israel? This is beyond pathetic. It's pathological."
The Syrian government and Hezbollah condemned the bombing.
Lebanese Prime Minister Najib Mikati, whose government includes ministers from Hezbollah, said his government was trying to identify the perpetrators and they would be punished.
Iran's Mehmanparast was quoted as calling for Lebanese national unity in the aftermath of the attack.
Hariri's son, Saad al-Hariri, accused Assad of being behind the bombing while March 14, a anti-Assad Lebanese political bloc, called Hassan "one of the martyrs of the independence uprising (against Syria)", adding that it was "a crime signed by Bashar Assad's regime, his regional allies and local tools".
The March 14 bloc called on Mikati's government to resign.
Speaking shortly after the bombing, Lebanese Foreign Minister Adnan Mansour told Reuters that his Iranian counterpart Ali Akbar Salehi had condemned the bombing and planned to visit Beirut on Saturday.
Iran has been a stalwart ally of Assad as he fights a 19-month-old uprising, counting his government and Hezbollah as part of an "axis of resistance" against Western and Israeli influence in the region.
Lebanon's religious communities are divided between those supporting Assad and those backing the Syrian rebels, leaving it vulnerable to spillover from the Syrian bloodshed.